Purdue University

Amptk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.

Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment

ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to identify key transcription factors between two GRNs.

Anchorwave is used for sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation.

ANGSD is a software for analyzing next generation sequencing data.

ANNOgesic is the swiss army knife for RNA-Seq based annotation of bacterial/archaeal genomes.

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

Another Bisulfite Mapping Algorithm (abismal) is a read mapping program for bisulfite sequencing in DNA methylation studies.

This module loads the ANSYS software suite which consists of programs that can be used to numerically simulate a large variety of structural and fluid dynamics problems found in many engineering, physics, medical, aeronautics and automotive industry applications.

This module enables the use of ANSYSEM, a popular Electromechanical application.

Antismash Antismash allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.

Anvio is an analysis and visualization platform for 'omics data.

Any2fasta can convert various sequence formats to FASTA.

The AOCC compiler system is a high performance, production quality code generation tool. The AOCC environment provides various options to developers when building and optimizing C, C++, and Fortran applications targeting 32-bit and 64-bit Linux® platforms.

AOCL are a set of numerical libraries tuned specifically for AMD EPYCTM processor family. They have a simple interface to take advantage of the latest hardware innovations.

archivemount is a FUSE-based file system for Unix variants, including Linux. Its purpose is to mount archives (e.g. tar, tar.gz, etc.) to a mount point where it can be read from or written to as with any other file system. This makes accessing the contents of the archive, which may be compressed, transparent to other programs, without decompressing them.

ARCS is a tool for scaffolding genome sequence assemblies using linked or long read sequencing data.

ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.